Wallasea island, Essex, where the earth from Crossrail's tunnel will be used to create a nature reserve. Photograph: Peter Macdiarmid/Getty Images

The first giant scoops of almost 5m tonnes of earth from deep beneath London were delivered to the Essex coast on Monday, the first step in creating the biggest man-made nature reserve in Europe.

The soil, excavated from two new 21km rail tunnels under the capital, will transform the pancake-flat intensive farmland of Wallasea Island into a labyrinth of mudflats, saltmarshes and lagoons last seen on the site 400 years ago.

The RSPB hopes the new reserve will see the return to England of lost breeding populations of spoonbills and Kentish plovers, as well as increasing already internationally important flocks of avocet, dunlin, redshank and lapwing, along with brent geese, wigeon and curlew in winter.

They expect saltwater fish such as bass, herring and flounder to use the wetland as a nursery, helping the small local seal colony, and plants such as samphire, sea lavender and sea aster are expected to thrive.

The island may have been first reclaimed from the sea by Dutch engineers centuries ago but was finally bulldozed flat 20 years ago to allow wheat and rape-growing. Surrounded by tall, grassy levees, it is now two metres below sea level at high tide and has a one in five risk of catastrophic flooding each year.

"It would have been enormously expensive to keep up the flood defences, with a real risk of major disaster," said the environment secretary, Owen Paterson. He said connecting the problem of what to do with the vast quantity of soil from the £14.8bn Crossrail project with the need of the RSPB to raise Wallasea island by two metres was "gain, gain, gain."

He added: "What it shows is that you should not be frightened of big infrastructure projects on environmental grounds. You can turn them to our advantage."

Four centuries ago there were 30,000 hectares of tidal salt marsh along the Essex coast but today just 2,500 hectares remain. "If you go back in time, a lot was clearly lost to farming and development," said Mike Clarke, RSPB chief executive. "But what we are losing it to now is mainly sea-level rise, running at 6mm a year. This is a race against time to put it back." Rising tides are expected to destroy 1,000 hectares of saltmarsh in next decade.

There are currently 30,000 birds living on a small 100-hectare saltmarsh in the area, but the new reserve will add 670 hectares and will include eight miles of walks and cycle paths. Building a new island will also protect other sites on the Essex coast, because if the area under sea level was flooded without being filled in, the huge currents would destroy existing mudflats around the island.

The soil is being dug from 20-30m below London and Crossrail says this is too deep for the earth to have been polluted. Of the 6m tonnes excavated, 75% will be shipped to a jetty on Wallasea Island and then on to an 800m conveyor belt. It will then be used to create the new landscape of winding creeks and mud islands. The earth from Crossrail's eastern tunnels will be loaded directly on to ships near Canning Town in east London, while dirt from the western tunnels will go by freight train to Northfleet in Kent and then on to ships. The last of more than 2,000 shiploads are expected to arrive in 2016, after which the RSPB will source other soil to complete the reserve.

Some wildlife already existed on the borders of the farmland and 800 common lizards and adders, 500 fish and a population of water voles have been moved to new habitats before the building work begins.

The Essex estuaries are among the most important coastal wetlands in the UK and are protected by national and European law.